BLASTP 2.2.26 [Sep-21-2011]
Reference: Altschul, Stephen F., Thomas L. Madden, Alejandro A. Schaffer,
Jinghui Zhang, Zheng Zhang, Webb Miller, and David J. Lipman (1997),
"Gapped BLAST and PSI-BLAST: a new generation of protein database search
programs", Nucleic Acids Res. 25:3389-3402.
Reference for compositional score matrix adjustment: Altschul, Stephen F.,
John C. Wootton, E. Michael Gertz, Richa Agarwala, Aleksandr Morgulis,
Alejandro A. Schaffer, and Yi-Kuo Yu (2005) "Protein database searches
using compositionally adjusted substitution matrices", FEBS J. 272:5101-5109.
Query= 032406
(141 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|2ZMV|A Chain A, Crystal Structure Of Synbindin
pdb|2ZMV|B Chain B, Crystal Structure Of Synbindin
Length = 227
Score = 140 bits (352), Expect = 3e-34, Method: Compositional matrix adjust.
Identities = 61/106 (57%), Positives = 82/106 (77%)
Query: 27 RMDTNDSLRVASLWHSMHAISQQLSPTTGCSGIELLEADTFDLHCFQSLTGTKFFVVCEP 86
R+ +N+ L +AS++HS+ AI QLSP G SGIE+LE DTF LHC+Q+LTG KF V+ +P
Sbjct: 102 RLTSNEKLMLASMFHSLFAIGSQLSPEQGSSGIEMLETDTFKLHCYQTLTGIKFVVLADP 161
Query: 87 GTQHMESLLKVIYELYTDYVLKNPFYEMEMPIRCELFDINLSQAVQ 132
++SLL+ IYE+Y+D+ LKNPFY +EMPIRCELFD NL A++
Sbjct: 162 RQAGIDSLLRKIYEIYSDFALKNPFYSLEMPIRCELFDQNLKLALE 207
Score = 30.0 bits (66), Expect = 0.42, Method: Compositional matrix adjust.
Identities = 11/19 (57%), Positives = 17/19 (89%)
Query: 3 AIYSLYIINKSGGLIFYKD 21
AI+S+Y++NK+GGLI+ D
Sbjct: 2 AIFSVYVVNKAGGLIYQLD 20
>pdb|2J3T|D Chain D, The Crystal Structure Of The Bet3-Trs33-Bet5-Trs23 Complex
Length = 219
Score = 140 bits (352), Expect = 3e-34, Method: Compositional matrix adjust.
Identities = 61/106 (57%), Positives = 82/106 (77%)
Query: 27 RMDTNDSLRVASLWHSMHAISQQLSPTTGCSGIELLEADTFDLHCFQSLTGTKFFVVCEP 86
R+ +N+ L +AS++HS+ AI QLSP G SGIE+LE DTF LHC+Q+LTG KF V+ +P
Sbjct: 102 RLTSNEKLMLASMFHSLFAIGSQLSPEQGSSGIEMLETDTFKLHCYQTLTGIKFVVLADP 161
Query: 87 GTQHMESLLKVIYELYTDYVLKNPFYEMEMPIRCELFDINLSQAVQ 132
++SLL+ IYE+Y+D+ LKNPFY +EMPIRCELFD NL A++
Sbjct: 162 RQAGIDSLLRKIYEIYSDFALKNPFYSLEMPIRCELFDQNLKLALE 207
Score = 30.0 bits (66), Expect = 0.44, Method: Compositional matrix adjust.
Identities = 11/19 (57%), Positives = 17/19 (89%)
Query: 3 AIYSLYIINKSGGLIFYKD 21
AI+S+Y++NK+GGLI+ D
Sbjct: 2 AIFSVYVVNKAGGLIYQLD 20
>pdb|3CUE|A Chain A, Crystal Structure Of A Trapp Subassembly Activating The
Rab Ypt1p
pdb|3CUE|G Chain G, Crystal Structure Of A Trapp Subassembly Activating The
Rab Ypt1p
pdb|3CUE|M Chain M, Crystal Structure Of A Trapp Subassembly Activating The
Rab Ypt1p
pdb|3CUE|S Chain S, Crystal Structure Of A Trapp Subassembly Activating The
Rab Ypt1p
Length = 219
Score = 57.0 bits (136), Expect = 3e-09, Method: Compositional matrix adjust.
Identities = 33/100 (33%), Positives = 49/100 (49%), Gaps = 24/100 (24%)
Query: 57 SGIELLEADTFDLHCFQSLTGTKFFVVC-------EP-----------------GTQHME 92
SG+ L D F + +Q+LTG KF + +P Q +
Sbjct: 117 SGLRQLCTDQFTMFIYQTLTGLKFVAISSSVMPQRQPTIATTDKPDRPKSTSNLAIQIAD 176
Query: 93 SLLKVIYELYTDYVLKNPFYEMEMPIRCELFDINLSQAVQ 132
+ L+ +Y LY+DYV+K+P Y MEMPIR LFD + + V+
Sbjct: 177 NFLRKVYCLYSDYVMKDPSYSMEMPIRSNLFDEKVKKMVE 216
Score = 43.5 bits (101), Expect = 4e-05, Method: Compositional matrix adjust.
Identities = 20/51 (39%), Positives = 36/51 (70%), Gaps = 1/51 (1%)
Query: 3 AIYSLYIINKSGGLIFYKDY-GSAGRMDTNDSLRVASLWHSMHAISQQLSP 52
AI ++ +INKSGGLI+ +++ ++++N+ L +AS H + AI+ QL+P
Sbjct: 2 AIETILVINKSGGLIYQRNFTNDEQKLNSNEYLILASTLHGVFAIASQLTP 52
>pdb|2J3T|C Chain C, The Crystal Structure Of The Bet3-Trs33-Bet5-Trs23 Complex
Length = 145
Score = 45.8 bits (107), Expect = 7e-06, Method: Compositional matrix adjust.
Identities = 30/134 (22%), Positives = 63/134 (47%), Gaps = 4/134 (2%)
Query: 3 AIYSLYIINKSGGLIFYKDY---GSAGRMDTNDSLRVASLWHSMHAISQQLSPTTGCSGI 59
+++LY+ +++G + Y ++ AG + + + S+ + ++SP G
Sbjct: 2 TVHNLYLFDRNGVCLHYSEWHRKKQAGIPKEEEYKLMYGMLFSIRSFVSKMSPLDMKDGF 61
Query: 60 ELLEADTFDLHCFQSLTGTKFFVVCEPGTQHMESLLKVIYE-LYTDYVLKNPFYEMEMPI 118
+ + LH +++ TG K + + G + +L IY LY ++V+KNP + +
Sbjct: 62 LSFQTSRYKLHYYETPTGIKVVMNTDLGVGPIRDVLHHIYSALYVEFVVKNPLCPLGQTV 121
Query: 119 RCELFDINLSQAVQ 132
+ ELF L V+
Sbjct: 122 QSELFRSRLDSYVR 135
>pdb|1H3Q|A Chain A, Crystal Sturcture Of Sedl At 2.4 Angstroms Resolution
Length = 140
Score = 31.6 bits (70), Expect = 0.17, Method: Compositional matrix adjust.
Identities = 13/34 (38%), Positives = 20/34 (58%), Gaps = 1/34 (2%)
Query: 91 MESLLKVIYELYTDYVLKNPFYEMEMPIRCELFD 124
+++ +Y+LY + + NPFYE PIR FD
Sbjct: 95 IKNFFTDVYDLYIKFAM-NPFYEPNSPIRSSAFD 127
>pdb|2J3W|A Chain A, The Crystal Structure Of The Bet3-Trs31-Sedlin Complex.
pdb|2J3W|C Chain C, The Crystal Structure Of The Bet3-Trs31-Sedlin Complex
Length = 142
Score = 31.2 bits (69), Expect = 0.18, Method: Compositional matrix adjust.
Identities = 13/34 (38%), Positives = 20/34 (58%), Gaps = 1/34 (2%)
Query: 91 MESLLKVIYELYTDYVLKNPFYEMEMPIRCELFD 124
+++ +Y+LY + + NPFYE PIR FD
Sbjct: 97 IKNFFTDVYDLYIKFAM-NPFYEPNSPIRSSAFD 129
>pdb|3EII|A Chain A, Zinc-Bound Glycoside Hydrolase 61 E From Thielavia
Terrestris
pdb|3EII|B Chain B, Zinc-Bound Glycoside Hydrolase 61 E From Thielavia
Terrestris
pdb|3EII|C Chain C, Zinc-Bound Glycoside Hydrolase 61 E From Thielavia
Terrestris
pdb|3EII|D Chain D, Zinc-Bound Glycoside Hydrolase 61 E From Thielavia
Terrestris
pdb|3EJA|A Chain A, Magnesium-Bound Glycoside Hydrolase 61 Isoform E From
Thielavia Terrestris
pdb|3EJA|B Chain B, Magnesium-Bound Glycoside Hydrolase 61 Isoform E From
Thielavia Terrestris
pdb|3EJA|C Chain C, Magnesium-Bound Glycoside Hydrolase 61 Isoform E From
Thielavia Terrestris
pdb|3EJA|D Chain D, Magnesium-Bound Glycoside Hydrolase 61 Isoform E From
Thielavia Terrestris
Length = 208
Score = 29.6 bits (65), Expect = 0.54, Method: Compositional matrix adjust.
Identities = 12/28 (42%), Positives = 17/28 (60%)
Query: 57 SGIELLEADTFDLHCFQSLTGTKFFVVC 84
SG LL A+ LH QS+ G +F++ C
Sbjct: 129 SGYYLLRAEQIGLHVAQSVGGAQFYISC 156
>pdb|1GKA|B Chain B, The Molecular Basis Of The Coloration Mechanism In
Lobster Shell. Beta-Crustacyanin At 3.2 A Resolution
Length = 174
Score = 26.6 bits (57), Expect = 4.3, Method: Compositional matrix adjust.
Identities = 11/34 (32%), Positives = 12/34 (35%)
Query: 23 GSAGRMDTNDSLRVASLWHSMHAISQQLSPTTGC 56
S D D R A W+ H I P T C
Sbjct: 13 ASVANQDNFDLRRYAGRWYQTHIIENAYQPVTRC 46
>pdb|3N29|A Chain A, Crystal Structure Of Carboxynorspermidine Decarboxylase
Complexed With Norspermidine From Campylobacter Jejuni
pdb|3N29|B Chain B, Crystal Structure Of Carboxynorspermidine Decarboxylase
Complexed With Norspermidine From Campylobacter Jejuni
Length = 418
Score = 26.6 bits (57), Expect = 5.5, Method: Compositional matrix adjust.
Identities = 13/49 (26%), Positives = 25/49 (51%), Gaps = 3/49 (6%)
Query: 58 GIELLEADTFDLHCFQSLTGTKFFVVCEPGTQHMESLLKVIYELYTDYV 106
GI + + DL+ ++ G F +CE +E++LKV E + ++
Sbjct: 182 GIRAKDFENVDLN---AIEGLHFHALCEESADALEAVLKVFEEKFGKWI 227
>pdb|3BOD|A Chain A, Structure Of Mouse Beta-Neurexin 1
Length = 178
Score = 25.8 bits (55), Expect = 9.6, Method: Compositional matrix adjust.
Identities = 24/82 (29%), Positives = 34/82 (41%), Gaps = 9/82 (10%)
Query: 2 AAIYSLYIINKSGGLIFYKDYGSAGRMDTN-DSLRVASLWHSMHAISQQLSPTTGCSGIE 60
A + S YI +K GG I YK + R T D L + A+ ++ ++G
Sbjct: 1 APLGSTYIFSKGGGQITYK-WPPNDRPSTRADRLAIGFSTVQKEAVLVRVDSSSGL---- 55
Query: 61 LLEADTFDLHCFQSLTGTKFFV 82
D +LH Q G KF V
Sbjct: 56 ---GDYLELHIHQGKIGVKFNV 74
Database: pdbaa
Posted date: Mar 3, 2013 10:34 PM
Number of letters in database: 14,973,337
Number of sequences in database: 62,578
Lambda K H
0.323 0.137 0.412
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 4,007,251
Number of Sequences: 62578
Number of extensions: 148124
Number of successful extensions: 317
Number of sequences better than 100.0: 13
Number of HSP's better than 100.0 without gapping: 7
Number of HSP's successfully gapped in prelim test: 6
Number of HSP's that attempted gapping in prelim test: 305
Number of HSP's gapped (non-prelim): 16
length of query: 141
length of database: 14,973,337
effective HSP length: 89
effective length of query: 52
effective length of database: 9,403,895
effective search space: 489002540
effective search space used: 489002540
T: 11
A: 40
X1: 16 ( 7.5 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (22.0 bits)
S2: 46 (22.3 bits)